From 53cc609c4ce28ab563d5d2de62b24a14d76354ed Mon Sep 17 00:00:00 2001
From: Axel Kohlmeyer <akohlmey@gmail.com>
Date: Thu, 3 May 2018 16:03:37 -0400
Subject: [PATCH] make filenames comply with LAMMPS conventions and add
reference log files
---
...{infromdata.class2 => in.large_nylon_melt} | 4 +-
.../log.20Apr18.large_nylon_melt.g++.1 | 170 ++++++++
.../log.20Apr18.large_nylon_melt.g++.4 | 170 ++++++++
.../{infromdata.class2 => in.tiny_nylon} | 2 +-
.../tiny_nylon/log.20Apr18.tiny_nylon.g++.1 | 365 ++++++++++++++++++
.../tiny_nylon/log.20Apr18.tiny_nylon.g++.4 | 365 ++++++++++++++++++
6 files changed, 1073 insertions(+), 3 deletions(-)
rename examples/USER/misc/bond_react/nylon,6-6_melt/{infromdata.class2 => in.large_nylon_melt} (92%)
create mode 100644 examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
create mode 100644 examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
rename examples/USER/misc/bond_react/tiny_nylon/{infromdata.class2 => in.tiny_nylon} (91%)
create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
create mode 100644 examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/infromdata.class2 b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
similarity index 92%
rename from examples/USER/misc/bond_react/nylon,6-6_melt/infromdata.class2
rename to examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
index 9d51b17b5d..072a8e3c45 100644
--- a/examples/USER/misc/bond_react/nylon,6-6_melt/infromdata.class2
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/in.large_nylon_melt
@@ -6,7 +6,7 @@ boundary p p p
atom_style full
-kspace_style pppm 1.0e-2 # actually, this appears required to check 1-3 neighbors
+kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
@@ -46,7 +46,7 @@ thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative
# restart 100 restart1 restart2
-run 200000
+run 200
# write_restart restart_longrun
# write_data restart_longrun.data
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
new file mode 100644
index 0000000000..f3b3840a92
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.1
@@ -0,0 +1,170 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+ orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 35200 atoms
+ reading velocities ...
+ 35200 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 31 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 33600 bonds
+ reading angles ...
+ 59200 angles
+ reading dihedrals ...
+ 80000 dihedrals
+ reading impropers ...
+ 35200 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 12
+ 25 angles with max type 24
+ 23 dihedrals with max type 33
+ 14 impropers with max type 9
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 11
+ 31 angles with max type 23
+ 39 dihedrals with max type 30
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 11
+ 25 angles with max type 23
+ 30 dihedrals with max type 30
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 13
+ 19 angles with max type 25
+ 16 dihedrals with max type 29
+ 10 impropers with max type 11
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.20765
+ grid = 18 18 18
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0333156
+ estimated relative force accuracy = 0.000100329
+ using double precision FFTs
+ 3d grid and FFT values/proc = 12167 5832
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 15 15 15
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 209.1 | 209.1 | 209.1 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 800 3666.3948 0.80366765 0 0
+ 50 673.95238 -9670.9169 0.80366765 31 0
+ 100 693.69241 -4696.4359 0.80366765 57 22
+ 150 715.44689 -14740.892 0.80366765 77 50
+ 200 721.16898 -1411.95 0.80366765 84 66
+Loop time of 107.389 on 1 procs for 200 steps with 35200 atoms
+
+Performance: 0.161 ns/day, 149.151 hours/ns, 1.862 timesteps/s
+99.7% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 27.191 | 27.191 | 27.191 | 0.0 | 25.32
+Bond | 11.46 | 11.46 | 11.46 | 0.0 | 10.67
+Kspace | 4.2507 | 4.2507 | 4.2507 | 0.0 | 3.96
+Neigh | 55.544 | 55.544 | 55.544 | 0.0 | 51.72
+Comm | 0.41715 | 0.41715 | 0.41715 | 0.0 | 0.39
+Output | 0.0011044 | 0.0011044 | 0.0011044 | 0.0 | 0.00
+Modify | 8.4756 | 8.4756 | 8.4756 | 0.0 | 7.89
+Other | | 0.04897 | | | 0.05
+
+Nlocal: 35200 ave 35200 max 35200 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 38406 ave 38406 max 38406 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 6.92787e+06 ave 6.92787e+06 max 6.92787e+06 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 6927872
+Ave neighs/atom = 196.815
+Ave special neighs/atom = 9.83489
+Neighbor list builds = 200
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+Total wall time: 0:01:48
diff --git a/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4 b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
new file mode 100644
index 0000000000..992a97e77e
--- /dev/null
+++ b/examples/USER/misc/bond_react/nylon,6-6_melt/log.20Apr18.large_nylon_melt.g++.4
@@ -0,0 +1,170 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# 35,000 atom nylon melt example
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data large_nylon_melt.data.gz
+ orthogonal box = (-2.68344 -2.06791 -2.21988) to (73.4552 73.2448 73.4065)
+ 2 by 1 by 2 MPI processor grid
+ reading atoms ...
+ 35200 atoms
+ reading velocities ...
+ 35200 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 31 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 33600 bonds
+ reading angles ...
+ 59200 angles
+ reading dihedrals ...
+ 80000 dihedrals
+ reading impropers ...
+ 35200 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 800.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 12
+ 25 angles with max type 24
+ 23 dihedrals with max type 33
+ 14 impropers with max type 9
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 11
+ 31 angles with max type 23
+ 39 dihedrals with max type 30
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 11
+ 25 angles with max type 23
+ 30 dihedrals with max type 30
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 13
+ 19 angles with max type 25
+ 16 dihedrals with max type 29
+ 10 impropers with max type 11
+
+thermo 50
+
+# dump 1 all xyz 100 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+# stable at 800K
+fix 1 statted_grp nvt temp 800 800 100
+
+# in order to customize behavior of reacting atoms,
+# you can use the internally created 'bond_react_MASTER_group', like so:
+# fix 2 bond_react_MASTER_group temp/rescale 1 800 800 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2] # cumulative reaction counts
+
+# restart 100 restart1 restart2
+
+run 200
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.20765
+ grid = 18 18 18
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0333156
+ estimated relative force accuracy = 0.000100329
+ using double precision FFTs
+ 3d grid and FFT values/proc = 4508 1620
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 15 15 15
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+Per MPI rank memory allocation (min/avg/max) = 81.11 | 81.13 | 81.15 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 800 3666.3948 0.80366765 0 0
+ 50 673.95238 -9670.9169 0.80366765 31 0
+ 100 693.69241 -4696.4359 0.80366765 57 22
+ 150 715.43654 -14742.205 0.80366765 77 50
+ 200 721.1906 -1411.4303 0.80366765 84 66
+Loop time of 56.2311 on 4 procs for 200 steps with 35200 atoms
+
+Performance: 0.307 ns/day, 78.099 hours/ns, 3.557 timesteps/s
+99.1% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 13.86 | 14.034 | 14.406 | 5.8 | 24.96
+Bond | 5.5592 | 5.5952 | 5.6492 | 1.4 | 9.95
+Kspace | 2.3969 | 2.7523 | 2.9203 | 12.5 | 4.89
+Neigh | 27.265 | 27.268 | 27.271 | 0.0 | 48.49
+Comm | 0.75523 | 0.77355 | 0.79381 | 1.7 | 1.38
+Output | 0.00051904 | 0.0007363 | 0.0013669 | 0.0 | 0.00
+Modify | 5.7629 | 5.7634 | 5.7641 | 0.0 | 10.25
+Other | | 0.04441 | | | 0.08
+
+Nlocal: 8800 ave 8912 max 8666 min
+Histogram: 1 0 0 1 0 0 0 0 1 1
+Nghost: 18358.8 ave 18432 max 18189 min
+Histogram: 1 0 0 0 0 0 0 0 1 2
+Neighs: 1.73197e+06 ave 1.77209e+06 max 1.68475e+06 min
+Histogram: 1 0 1 0 0 0 0 0 0 2
+
+Total # of neighbors = 6927873
+Ave neighs/atom = 196.815
+Ave special neighs/atom = 9.83489
+Neighbor list builds = 200
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+Total wall time: 0:00:57
diff --git a/examples/USER/misc/bond_react/tiny_nylon/infromdata.class2 b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
similarity index 91%
rename from examples/USER/misc/bond_react/tiny_nylon/infromdata.class2
rename to examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
index 9efc7ec98f..3e21f69331 100644
--- a/examples/USER/misc/bond_react/tiny_nylon/infromdata.class2
+++ b/examples/USER/misc/bond_react/tiny_nylon/in.tiny_nylon
@@ -7,7 +7,7 @@ boundary p p p
atom_style full
-kspace_style pppm 1.0e-2 # actually, this appears required to make LAMMPS to check 1-3 neighbors
+kspace_style pppm 1.0e-4
pair_style lj/class2/coul/long 8.5
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
new file mode 100644
index 0000000000..a65a5306f3
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.1
@@ -0,0 +1,365 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+ orthogonal box = (-25 -25 -25) to (25 25 25)
+ 1 by 1 by 1 MPI processor grid
+ reading atoms ...
+ 44 atoms
+ reading velocities ...
+ 44 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 29 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 42 bonds
+ reading angles ...
+ 74 angles
+ reading dihedrals ...
+ 100 dihedrals
+ reading impropers ...
+ 44 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 14
+ 25 angles with max type 28
+ 23 dihedrals with max type 36
+ 14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 13
+ 31 angles with max type 27
+ 39 dihedrals with max type 33
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 13
+ 25 angles with max type 27
+ 30 dihedrals with max type 33
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 15
+ 19 angles with max type 29
+ 16 dihedrals with max type 32
+ 10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.0534597
+ grid = 2 2 2
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0402256
+ estimated relative force accuracy = 0.000121138
+ using double precision FFTs
+ 3d grid and FFT values/proc = 343 8
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 10 10 10
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+WARNING: Inconsistent image flags (../domain.cpp:786)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.34 | 33.34 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 300 346.78165 0.0034851739 0 0
+ 50 296.70408 -51.30066 0.0034851739 1 0
+ 100 275.26011 39.120329 0.0034851739 1 1
+ 150 438.68516 35.257539 0.0034851739 1 1
+ 200 394.48971 15.444537 0.0034851739 1 1
+ 250 356.00369 50.185792 0.0034851739 1 1
+ 300 301.25816 -26.891497 0.0034851739 1 1
+ 350 279.17264 12.694513 0.0034851739 1 1
+ 400 248.71641 10.684558 0.0034851739 1 1
+ 450 240.30602 12.963034 0.0034851739 1 1
+ 500 252.71279 0.91620356 0.0034851739 1 1
+ 550 300.56824 18.541436 0.0034851739 1 1
+ 600 306.46441 -1.9736081 0.0034851739 1 1
+ 650 336.4537 21.474831 0.0034851739 1 1
+ 700 323.46217 8.486376 0.0034851739 1 1
+ 750 271.87146 5.9615231 0.0034851739 1 1
+ 800 268.43041 36.676068 0.0034851739 1 1
+ 850 269.02683 7.6295416 0.0034851739 1 1
+ 900 282.03605 -1.4688833 0.0034851739 1 1
+ 950 243.69136 -22.771489 0.0034851739 1 1
+ 1000 285.01348 17.925748 0.0034851739 1 1
+ 1050 383.47985 0.70536985 0.0034851739 1 1
+ 1100 368.97167 -4.3046933 0.0034851739 1 1
+ 1150 373.64459 6.3491837 0.0034851739 1 1
+ 1200 332.90575 -36.501095 0.0034851739 1 1
+ 1250 314.04078 -13.382767 0.0034851739 1 1
+ 1300 305.84166 4.7713641 0.0034851739 1 1
+ 1350 286.22145 37.621803 0.0034851739 1 1
+ 1400 265.52855 23.621002 0.0034851739 1 1
+ 1450 281.807 -31.266828 0.0034851739 1 1
+ 1500 275.33855 33.495565 0.0034851739 1 1
+ 1550 273.04973 -22.913871 0.0034851739 1 1
+ 1600 308.18478 -17.98151 0.0034851739 1 1
+ 1650 333.27664 28.987529 0.0034851739 1 1
+ 1700 296.16091 -1.1440455 0.0034851739 1 1
+ 1750 365.75611 34.574845 0.0034851739 1 1
+ 1800 292.83503 -33.199654 0.0034851739 1 1
+ 1850 261.50282 42.608703 0.0034851739 1 1
+ 1900 315.14188 -31.058803 0.0034851739 1 1
+ 1950 335.12895 12.40597 0.0034851739 1 1
+ 2000 278.08586 -5.3178633 0.0034851739 1 1
+ 2050 283.23847 -3.3974302 0.0034851739 1 1
+ 2100 281.38904 0.70263324 0.0034851739 1 1
+ 2150 302.23197 23.372316 0.0034851739 1 1
+ 2200 337.49259 -4.8716803 0.0034851739 1 1
+ 2250 409.64134 -12.043721 0.0034851739 1 1
+ 2300 309.21764 -21.824645 0.0034851739 1 1
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+ 10000 401.93365 -7.637581 0.0034851739 1 1
+Loop time of 1.94139 on 1 procs for 10000 steps with 44 atoms
+
+Performance: 445.042 ns/day, 0.054 hours/ns, 5150.945 timesteps/s
+99.3% CPU use with 1 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.26479 | 0.26479 | 0.26479 | 0.0 | 13.64
+Bond | 0.76875 | 0.76875 | 0.76875 | 0.0 | 39.60
+Kspace | 0.32111 | 0.32111 | 0.32111 | 0.0 | 16.54
+Neigh | 0.41333 | 0.41333 | 0.41333 | 0.0 | 21.29
+Comm | 0.025956 | 0.025956 | 0.025956 | 0.0 | 1.34
+Output | 0.0043445 | 0.0043445 | 0.0043445 | 0.0 | 0.22
+Modify | 0.12526 | 0.12526 | 0.12526 | 0.0 | 6.45
+Other | | 0.01786 | | | 0.92
+
+Nlocal: 44 ave 44 max 44 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Nghost: 62 ave 62 max 62 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+Neighs: 812 ave 812 max 812 min
+Histogram: 1 0 0 0 0 0 0 0 0 0
+
+Total # of neighbors = 812
+Ave neighs/atom = 18.4545
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+Total wall time: 0:00:01
diff --git a/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4 b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
new file mode 100644
index 0000000000..dddc9f2801
--- /dev/null
+++ b/examples/USER/misc/bond_react/tiny_nylon/log.20Apr18.tiny_nylon.g++.4
@@ -0,0 +1,365 @@
+LAMMPS (20 Apr 2018)
+OMP_NUM_THREADS environment is not set. Defaulting to 1 thread. (../comm.cpp:90)
+ using 1 OpenMP thread(s) per MPI task
+# two monomer nylon example
+# reaction produces a condensed water molecule
+
+units real
+
+boundary p p p
+
+atom_style full
+
+kspace_style pppm 1.0e-4
+
+pair_style lj/class2/coul/long 8.5
+
+angle_style class2
+
+bond_style class2
+
+dihedral_style class2
+
+improper_style class2
+
+read_data tiny_nylon.data
+ orthogonal box = (-25 -25 -25) to (25 25 25)
+ 1 by 2 by 2 MPI processor grid
+ reading atoms ...
+ 44 atoms
+ reading velocities ...
+ 44 velocities
+ scanning bonds ...
+ 9 = max bonds/atom
+ scanning angles ...
+ 21 = max angles/atom
+ scanning dihedrals ...
+ 29 = max dihedrals/atom
+ scanning impropers ...
+ 29 = max impropers/atom
+ reading bonds ...
+ 42 bonds
+ reading angles ...
+ 74 angles
+ reading dihedrals ...
+ 100 dihedrals
+ reading impropers ...
+ 44 impropers
+ 4 = max # of 1-2 neighbors
+ 6 = max # of 1-3 neighbors
+ 12 = max # of 1-4 neighbors
+ 41 = max # of special neighbors
+
+velocity all create 300.0 4928459 dist gaussian
+
+molecule mol1 rxn1_stp1_unreacted.data_template
+Read molecule mol1:
+ 18 atoms with max type 8
+ 16 bonds with max type 14
+ 25 angles with max type 28
+ 23 dihedrals with max type 36
+ 14 impropers with max type 11
+molecule mol2 rxn1_stp1_reacted.data_template
+Read molecule mol2:
+ 18 atoms with max type 9
+ 17 bonds with max type 13
+ 31 angles with max type 27
+ 39 dihedrals with max type 33
+ 20 impropers with max type 1
+molecule mol3 rxn1_stp2_unreacted.data_template
+Read molecule mol3:
+ 15 atoms with max type 9
+ 14 bonds with max type 13
+ 25 angles with max type 27
+ 30 dihedrals with max type 33
+ 16 impropers with max type 1
+molecule mol4 rxn1_stp2_reacted.data_template
+Read molecule mol4:
+ 15 atoms with max type 11
+ 13 bonds with max type 15
+ 19 angles with max type 29
+ 16 dihedrals with max type 32
+ 10 impropers with max type 13
+
+thermo 50
+
+# dump 1 all xyz 1 test_vis.xyz
+
+fix myrxns all bond/react stabilization yes statted_grp .03 react rxn1 all 1 2.9 mol1 mol2 rxn1_stp1_map react rxn2 all 1 5 mol3 mol4 rxn1_stp2_map
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+dynamic group bond_react_MASTER_group defined
+dynamic group statted_grp defined
+
+fix 1 statted_grp nvt temp 300 300 100
+
+fix 4 bond_react_MASTER_group temp/rescale 1 300 300 10 1
+
+thermo_style custom step temp press density f_myrxns[1] f_myrxns[2]
+
+# restart 100 restart1 restart2
+
+run 10000
+PPPM initialization ...
+ using 12-bit tables for long-range coulomb (../kspace.cpp:321)
+ G vector (1/distance) = 0.0534597
+ grid = 2 2 2
+ stencil order = 5
+ estimated absolute RMS force accuracy = 0.0402256
+ estimated relative force accuracy = 0.000121138
+ using double precision FFTs
+ 3d grid and FFT values/proc = 252 2
+Neighbor list info ...
+ update every 1 steps, delay 10 steps, check yes
+ max neighbors/atom: 2000, page size: 100000
+ master list distance cutoff = 10.5
+ ghost atom cutoff = 10.5
+ binsize = 5.25, bins = 10 10 10
+ 2 neighbor lists, perpetual/occasional/extra = 1 1 0
+ (1) pair lj/class2/coul/long, perpetual
+ attributes: half, newton on
+ pair build: half/bin/newton
+ stencil: half/bin/3d/newton
+ bin: standard
+ (2) fix bond/react, occasional, copy from (1)
+ attributes: half, newton on
+ pair build: copy
+ stencil: none
+ bin: none
+WARNING: Inconsistent image flags (../domain.cpp:786)
+Per MPI rank memory allocation (min/avg/max) = 33.34 | 33.69 | 34.37 Mbytes
+Step Temp Press Density f_myrxns[1] f_myrxns[2]
+ 0 300 346.78165 0.0034851739 0 0
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+ 100 275.26011 39.120329 0.0034851739 1 1
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+ 250 356.00369 50.185792 0.0034851739 1 1
+ 300 301.25816 -26.891497 0.0034851739 1 1
+ 350 279.17264 12.694513 0.0034851739 1 1
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+ 650 336.4537 21.474831 0.0034851739 1 1
+ 700 323.46217 8.486376 0.0034851739 1 1
+ 750 271.87146 5.9615231 0.0034851739 1 1
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+ 8700 286.54284 -31.490479 0.0034851739 1 1
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+ 8950 341.08296 2.80127 0.0034851739 1 1
+ 9000 403.71266 17.88418 0.0034851739 1 1
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+ 9100 307.98322 16.707575 0.0034851739 1 1
+ 9150 276.75719 -35.563923 0.0034851739 1 1
+ 9200 230.15547 3.8091656 0.0034851739 1 1
+ 9250 264.64479 -20.97438 0.0034851739 1 1
+ 9300 285.70467 13.881735 0.0034851739 1 1
+ 9350 297.515 13.599319 0.0034851739 1 1
+ 9400 341.45203 -28.494544 0.0034851739 1 1
+ 9450 319.29703 -27.907344 0.0034851739 1 1
+ 9500 332.50473 4.9891138 0.0034851739 1 1
+ 9550 293.10499 -8.3244772 0.0034851739 1 1
+ 9600 255.31174 2.2568315 0.0034851739 1 1
+ 9650 250.01932 5.7005159 0.0034851739 1 1
+ 9700 278.37409 -8.5970424 0.0034851739 1 1
+ 9750 294.86737 17.686447 0.0034851739 1 1
+ 9800 277.07345 -2.0856886 0.0034851739 1 1
+ 9850 295.54707 2.8365471 0.0034851739 1 1
+ 9900 311.51074 29.885116 0.0034851739 1 1
+ 9950 296.01363 12.206068 0.0034851739 1 1
+ 10000 341.35187 -3.0045464 0.0034851739 1 1
+Loop time of 3.64332 on 4 procs for 10000 steps with 44 atoms
+
+Performance: 237.146 ns/day, 0.101 hours/ns, 2744.751 timesteps/s
+94.5% CPU use with 4 MPI tasks x 1 OpenMP threads
+
+MPI task timing breakdown:
+Section | min time | avg time | max time |%varavg| %total
+---------------------------------------------------------------
+Pair | 0.0029962 | 0.10426 | 0.34564 | 43.9 | 2.86
+Bond | 0.005929 | 0.29803 | 0.95305 | 71.2 | 8.18
+Kspace | 0.83969 | 1.5992 | 1.9344 | 35.6 | 43.89
+Neigh | 0.65468 | 0.66443 | 0.67431 | 0.9 | 18.24
+Comm | 0.1727 | 0.23754 | 0.2745 | 8.0 | 6.52
+Output | 0.0048738 | 0.010774 | 0.028434 | 9.8 | 0.30
+Modify | 0.62478 | 0.70376 | 0.779 | 6.5 | 19.32
+Other | | 0.02531 | | | 0.69
+
+Nlocal: 11 ave 40 max 0 min
+Histogram: 2 1 0 0 0 0 0 0 0 1
+Nghost: 36 ave 47 max 7 min
+Histogram: 1 0 0 0 0 0 0 0 0 3
+Neighs: 203 ave 809 max 0 min
+Histogram: 3 0 0 0 0 0 0 0 0 1
+
+Total # of neighbors = 812
+Ave neighs/atom = 18.4545
+Ave special neighs/atom = 9.77273
+Neighbor list builds = 10000
+Dangerous builds = 0
+
+# write_restart restart_longrun
+# write_data restart_longrun.data
+Total wall time: 0:00:03
--
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